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Bioinformatics Advance Access originally published online on July 26, 2005
Bioinformatics 2005 21(19):3719-3725; doi:10.1093/bioinformatics/bti595
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

CHORAL: a differential geometry approach to the prediction of the cores of protein structures

Rinaldo W. Montalvão *, Richard E. Smith , Simon C. Lovell {dagger} and Tom L. Blundell

Department of Biochemistry, University of Cambridge Tennis Court Road, Cambridge CB2 1GA, UK

*To whom correspondence should be addressed.

Motivation: Although the cores of homologous proteins are relatively well conserved, amino acid substitutions lead to significant differences in the structures of divergent superfamilies. Thus, the classification of amino acid sequence patterns and the selection of appropriate fragments of the protein cores of homologues of known structure are important for accurate comparative modelling.

Results: CHORAL utilizes a knowledge-based method comprising an amalgam of differential geometry and pattern recognition algorithms to identify conserved structural patterns in homologous protein families. Propensity tables are used to classify and to select patterns that most likely represent the structure of the core for a target protein. In our benchmark, CHORAL demonstrates a performance equivalent to that of MODELLER.

Availability: The algorithm is available via internet on http://www-cryst.bioc.cam.ac.uk/servers.html

Contact: rinaldo{at}cryst.bioc.cam.ac.uk

Received on June 2, 2005; revised on July 21, 2005; accepted on July 21, 2005

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